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Our model's predictions agree well with experimentally derived transcription levels in the mitochondria of frog, human and rat, including disease states such as the MELAS syndrome in human and the hypothyroid condition in rat.
Although several functions of the Hivep paralogs have been demonstrated in the fruitfly, Xenopus frog, human, and mouse (Wu 2002), the Hivep paralogs have, so far, not been examined in teleost fishes.
For constructing a molecular phylogenetic tree for FAS and FADD proteins, we used Fas and FADD sequences manually predicted from the chicken, zebrafish and stickleback genomes together with published catfish (Ictalurus punctatus), frog, human and mouse Fas and FADD sequences [ 9, 10, 35- 40] [see Additional file 7].
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RRTs were performed on the protein sequences of 623 orthologous genes, with Banna caecilian, Western clawed frog and human as the ingroups and Indonesian coelacanth as the outgroup.
Note these results are consistent with those of Patel et al. [ 11], who report that MPG and C16orf35 surround the α hemoglobin gene cluster in frog, chicken and human, and one of the α and β hemoglobin clusters in platypus and opposum.
We also performed an RRT on a carefully curated dataset consisting of 623 orthologous genes, in which caecilian, frog and human were used as the ingroups and coelacanth was used as the outgroup.
The deduced CpC8α exhibits 89%, 49% and 44% identity with nurse shark, frog and human orthologs, respectively.
Ostrich ADH2 shares 81.6%, 77.3% and 68.8% identity with turtle, frog and human ADH2, respectively.
There are much fewer LIRs in yeast, fruitfly, pufferfish and chicken than in Caenorhabditis elegans, zebrafish, frog and human.
Sequence data from complete genomes of tetrapods such as mouse, frog and human as well as from invertebrates such as Caenorhabditis elegans and Drosophila melanogaster show that many gene families tend to be larger in vertebrates [ 7- 9].
They are not: both frogs and humans (and birds and lizards and cats) are equally closely related to fishes because as tetrapods they share a common ancestor to the exclusion of bony fishes.
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